Potential of Bacillus paramycoides hydrolase to degrade propiconazole

Amino acids (N)	932
Molecular weight	1869.85
Theoretical pI	5.18
Negatively charged residues (N)	127
Positively charged resides (N)	90
Formula	C₄₄₉₂H₇₂₃₀N₁₂₅₈O₁₃₉₀S₂₄
Total No. of atoms	14394
Ext. coefficient	26025
Estimated half-life	30 h (mammalian reticulocytes, in vitro) >20 h (yeast, in vivo) >10 h (Escherichia coli, in vivo)
Instability index	38.07
Aliphatic index	100.71
Grand average of hydropathicity	−0.095

Table 2

Secondary structure predicted with SOPMA

Alpha helix	Extended strands	Beta turns	Random coils
41.64 %	19.24 %	7.57 %	31.55 %

3D structure of hydrolase generated by the SWISS-MODEL tool. The purple region shows the Hsp70 chaperone of *E. coli* for the production of stable conjugate protein complex

Ramachandran plot of hydrolase from *Bacillus paramycoides*

Table 3

Active site prediction with Discovery Studio

Sites	Dimensions XYZ	Point Count
Site 1	12.779000 / 8.882247 / −8.610573	5407
Site 2	−3.971000 / −3.617753 / 1.139427	1330
Site 3	−5.721000 / 12.132247 / −2.110573	708

Table 4

Selected propiconazole and its derivatives

Ser. no.	Compound name	PubChem CID	Formula
1	(2R,4S)-2-(2,4-Dichlorophenyl)- 4-propyl-2-[(1H-1,2,4-triazol-1-yl) methyl]-1,3-dioxolane	679162	C₁₅H₁₇Cl₂N₃O₂
2	1-[[(2S,4S)-2-(2,4-dichlorophenyl)- 4-propyl-1,3-dioxolan-2-yl]methyl]- 1,2,4-triazole	679164	C₁₅H₁₇Cl₂N₃O₂
3	1-[[2-(2,4-Dichlorophenyl)-4- (2,2,3,3,3-pentadeuteriopropyl)-1,3- dioxolan-2-yl]methyl]-1,2,4-triazole	129318213	C₁₅H₁₇Cl₂N₃O₂
4	Hispor	156985	C₂₄H₂₆Cl₂N₆O₄
5	Propiconazole 4,4′-dihydroxybiphenyl	86643422	C₂₇H₂₇Cl₂N₃O₄
6	Propiconazole hydrochloride	129773016	C₁₅H₁₈Cl₃N₃O₂
7	Propiconazole TP1	155884399	C₁₃H₁₁Cl₂N₃O₄
8	Propiconazole TP2	703104	C₁₀H₉Cl₂N₃O
9	Propiconazole-(phenyl-d3)	124202653	C₁₅H₁₇Cl₂N₃O₂
10	Propiconazole	43234	C₁₅H₁₇Cl₂N₃O₂
11	Propiconazole-d7	71751781	C₁₅H₁₇Cl₂N₃O₂

Table 5

Binding energies and types of intermolecular interactions of compounds with hydrolase

Compounds	Molecular weight (g/mol)	Energy (kcal/mol)
1-[[(2S,4S)-2-(2,4-dichlorophenyl)-4-propyl-1,3-dioxolan-2-yl] methyl]-1,2,4-triazole	342.2	−6.8
Propiconazole TP1	344.15	−6.6
1-[[2-(2,4-Dichlorophenyl)-4-(2,2,3,3,3-pentadeuteriopropyl)-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole	347.2	−6.2
Propiconazole	342.2	−6.2
(2R,4S)-2-(2,4-Dichlorophenyl)-4-propyl-2-[(1H-1,2,4-triazol-1-yl)methyl]-1,3-dioxolane	342.2	−6.1
Hispor	533.4	−6.1
Propiconazole-d7	349.3	−6.0
Propiconazole 4,4′-dihydroxybiphenyl	528.4	−5.9
Propiconazole hydrochloride	378.7	−5.9
Propiconazole-(phenyl-d3)	345.2	−5.8
Propiconazole TP2	258.1	−5.7

Interaction between hydrolase and (2R,4S)-2-(2,4-dichlorophenyl)-4-propyl-2-[(1H-1,2,4-triazol-1-yl)methyl]-1,3-dioxolane complex 1 visualised with PyMOL

Interaction between hydrolase and 1-[[2-(2,4-dichlorophenyl)-4-(2,2,3,3,3-pentadeuteriopropyl)-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole complex 2 visualised with PyMOL

Interaction between hydrolase and 1-[[(2S,4S)-2-(2,4-dichlorophenyl)-4-propyl-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole complex 3 visualised with PyMOL

Interaction between hydrolase and propiconazole 4,4’-dihydroxybiphenyl complex 4 visualised with PyMOL

Interaction between hydrolase and propiconazole hydrochloride complex 5 visualised with PyMOL

Interaction between hydrolase and propiconazole-d7 complex 6 visualised with PyMOL

Interaction between hydrolase and propiconazole complex 7 visualised with PyMOL

Interaction between hydrolase and propiconazole TP1 complex 8 visualised with PyMOL

Mutated structure of hydrolase from *Bacillus paramycoides*

Interaction between hydrolase and propiconazole TP1. The ligand is positioned within the active site and stabilised by key catalytic residues, including His66, His67, and Trp92. Additional residues such as Phe13, Val15, Lys130, and Thr131 contribute through hydrophobic contacts and hydrogen bonding. Green lines represent hydrogen bonds, magenta lines hydrophobic and π–π interactions

Interaction between mutated hydrolase and 1-[[2-(2,4-dichlorophenyl)-4-(2,2,3,3,3-pentadeuteriopropyl)-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole

Interaction between mutated hydrolase and 1-[[(2S,4S)-2-(2,4-dichlorophenyl)-4-propyl-1,3-dioxolan-2-yl] methyl]-1,2,4-triazole

Table 6

Identified mutations and classification of mutants in silico

Metallo-ß-lactamase fold metallo-hydrolase by species	Accession number	Amino acid substituted	Mutation position	Amino acid replaced with	I-mutant results	MU-PRO result	PHD-SNP results	SIFT results
Bacillus paramycoides	WP_178938973.1	D	151	E	Increase	Increase	Neutral	Neutral
Bacillus cereus	WP_193645052.1	N	82	K	Decrease	Decrease	Deleterious	Deleterious
Bacillus mycoides	WP_215554119.1	V	238	M	Decrease	Decrease	Deleterious	Neutral
Bacillus thuringiensis	WP_264539129.1	D	123	G	Decrease	Decrease	Neutral	Deleterious
Bacillus nitratireducens	WP_044737773.1	L	312	W	Decrease	Increase	Neutral	Deleterious
Bacillus sp. CDB3	WP_128853480.1	H	47	Q	Decrease	Increase	Deleterious	Neutral
Bacillus sp. TH12	WP_201056898.1	A	119	V	Increase	Increase	Neutral	Neutral
Bacillus sp. NP247	WP_219920057.1	V	50	A	Decrease	Decrease	Deleterious	Deleterious
Bacillus sp. MYb209	WP_105584583.1	T	33	I	Decrease	Decrease	Neutral	Neutral
Bacillus toyonensis	WP_097999873.1	K	108	R	Decrease	Decrease	Neutral	Neutral

Table 7

Docking and interaction study of hydrolase with the best three propiconazole derivatives

Pollutants	Docking energies (kcal/mol)	Amino acid residues	Distance between interacting amino acid residues (Å)	Type of bond interaction
Propiconazole TP1	−7.4	HIS66, TRP92, HIS67, VAL15, THR131, PHE13, LYS130	2.84, 2.93, 3.14, 4.26, 5.01, 4.92, 4.67, 4.99, 5.23, 3.02	Alkyl, pi-alkyl, conventional, Pi-Pi T-shaped, hydrogen bonds, Van der Waals forces
1-[[(2S,4S)-2-(2,4-dichlorophenyl)-4-propyl-1,3-dioxolan-2-yl] methyl]-1,2,4-triazole	−7.1	HIS67, HIS66, TRP92, ILE192, ALA165, HIS164, HIS65	3.94, 4.85, 4.71, 4.31, 4.57, 3.68	Pi-lone pair, Pi-alkyl, Pi-Pi T-shaped, Van der Waals forces
1-[[2-(2,4-Dichlorophenyl)-4-(2,2,3,3,3-pentadeuteriopropyl)-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole	−7.1	ILE194, HIS164, ASP183, ALA165, TYR139 HIS67, HIS66, HIS65,	4.42, 2.95, 2.75, 4.44, 5.50, 5.41, 3.76, 4.82, 2.70, 3.61, 2.08	Alkyl, pi-alkyl, conventional, Pi-Pi T-shaped, carbon, Waals forces hydrogen bonds, Van der

Protein–ligand complex analysis in molecular dynamics simulation. A) Root mean square deviation (RMSD) shows the overall structural stability of the complex by tracking backbone fluctuations over time. B) Radius of gyration (Rg) shows the compactness and structural integrity of the protein; consistent Rg values suggest a stable and well-folded conformation. C) Root mean square fluctuation (RMSF) highlights residue-specific flexibility, identifying regions with higher mobility such as loops, binding pockets, or terminal ends. D) Principal component analysis (PCA) illustrates dominant collective motions and major conformational transitions of the complex, helping to visualise large-scale structural dynamics that influence ligand binding and enzyme function

Distance analysis between the ligand and key protein residues in molecular dynamics simulation. A) Ligand-catalytic residue distances are consistently short (0.98–2.89 Å), which indicates stable interactions, essential for catalytic activity and effective binding. B) Significantly larger separation between the ligand and selected, non-catalytic residues (25.83–28.99 Å) confirms that these residues do not directly participate in ligand interaction and remain structurally distant throughout the simulation

Table 8

MM/GBSA complex–receptor–ligand energy decomposition

Energy component	Average	SD	SEM
VDWAALS	−39.6668	5.9813	1.8915
EEL	−0.6035	2.2259	0.7039
EGB	8.0517	2.9888	0.9451
ESURF	−3.6938	0.5431	0.1718
DELTA G gas	−40.2703	5.9055	1.8675
DELTA G solv	4.3579	3.1938	1.0100
DELTA TOTAL	−35.9124	6.4629	2.0437

[i] MM/GBPSA – molecular mechanics / generalised born surface areas; SD – standard deviation; SEM – standard error of the mean

Table 9

MM/PBSA complex–receptor–ligand energy decomposition

Energy component	Average	SD	SEM
VDWAALS	−39.6668	5.9813	1.8915
EEL	−0.6035	2.2259	0.7039
EPB	12.9297	5.5557	1.7569
ENPOLAR	−21.1805	3.2240	1.0195
EDISPER	41.7699	4.0950	1.2950
DELTA G gas	−40.2703	5.9055	1.8675
DELTA G solv	33.5192	6.0584	1.9158
DELTA TOTAL	−6.7511	7.0464	2.2283

[i] MM/PBSA – molecular mechanics / Poisson-Boltzman surface areas; SD – standard deviation; SEM – standard error of the mean

References

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Articles in this issue

DOI: https://doi.org/10.2478/aiht-2026-77-4001 | Journal eISSN: 1848-6312 (formerly 0004-1254) | Journal ISSN: 0004-1254

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Language: English, Croatian

Page range: 9 - 20

Submitted on: May 1, 2025

Accepted on: Mar 1, 2026

Published on: Mar 30, 2026

Published by: Institute for Medical Research and Occupational Health

In partnership with: Paradigm Publishing Services

Keywords:

bioremediation,

environmental toxicology,

hydrolase enzymes,

molecular docking,

propiconazole degradation

Related subjects:

Medicine,

Basic medical science,

Basic medical science, other

© 2026 Muhammad Naveed, Maida Salah Ud Din, Tariq Aziz, Rida Naveed, Daochen Zhu, Maha Alharbi, Ashwag Shami, published by Institute for Medical Research and Occupational Health
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 77 (2026): Issue 1 (March 2026)

Potential of Bacillus paramycoides hydrolase to degrade propiconazole

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